Internet Resource Guide

A Compilation of Essential Websites for

Penn State B.S. Biology Majors

Provided By: Larry Klomps

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Table of Contents

Information About This Guide...............................................................3

Intended Audience & Purpose................................................................3

Content and Material ..............................................................................3

Assumptions about the Reader ...............................................................4

Guide Organization.................................................................................4

Hints and Tips.........................................................................................5

Resources Found in this Guide................................................................5

General Internet Sites...............................................................................6

RCSB Protein Data Bank...............................................................6

PROSITE Protein Database...........................................................7

BioOne.......................................................................................... 8

Biology News Net..........................................................................9

Publications..........................................................................................10

Journal of Cell Biology.................................................................10

Thomson Reuters Web of KnowledgeSM

.......................................11

The Statistical Abstract of the United States.................................12

Catalog of U.S. Government Publications....................................13

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Information About this Guide

This section provides information about what one can expect to find relevant to

one's field of study, research, or work in this guide. Thus, it will introduce who

should read this guide, its content and organization, and prior knowledge needed to

use this guide effectively.

Intended Audience & Purpose

The purpose of this resource guide is to provide a collection of practical internet

resources for undergraduate students majoring in biology at Penn State. Students

who are in 5th semester standing or higher may find this guide more useful than a

freshman biology student due to advanced subject matter. However, underclassman

can still benefit from the content provided in this document, such as sites for

researching various topics. That being said, this guide will offer valuable reference

materials to enhance productivity for students at different points in their studies.

Content and Material

This guide includes multiple links to web sites that a biology student would find

important to his or her everyday studies. Some subject matter in these sites include

biochemistry and molecular biology, cell biology, proteomics, microbiology, and

ecology. Also incorporated into this guide are links to journals for students

conducting research that are in need of primary literature. Likewise, one can

exploit the aforementioned resources or see what cutting-edge research is taking

place with additional links to scientific news and discussion boards.

About this Guide

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Assumptions about the Reader

It is recommended that readers of this guide are biology majors or were previously

enrolled in related coursework. Some suggested PSU courses that are necessary in

understanding the material presented in this guide are BMB 401, CHEM 212,

BIOL 110, 230, and 240. If one has not yet completed these classes or is currently

enrolled in one, there is still plenty of useful resources in this guide to aid the

developing biologist. If one cannot understand a topic, look it up, biology is an

investigative science!

Guide Organization

The most efficient way to use this guide is to refer to the headings listed in the

Table of Contents. The resources in this guide are divided into two broad

categories: General Internet Sites and Publications. Provided under these two

sections are four web sites with brief abstracts that offer pointers about each site

and highlights unique attributes of those sites.

Finding good publications can be a real pain. Thus, a guide that offers sites to

reduce the headaches associated with finding good publications is essential to any

student doing research. Sites intended for upperclassmen use are listed first, with

subsequent sites accommodating students at different levels of biological

coursework.

About this Guide

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Hints and Tips

Being a Penn State student comes with a multitude of resources available

both on and off campus, especially for biology students. To ensure student

awareness of these resources, this guide will use three distinctive pictures for

sites specific to Penn State students.

o This caption will appear by sites that contain databases of

publications. Students involved with research are encouraged to take

advantage of the wealth of primary literature available to them for

citing sources applicable to their own.

o There are a lot of interesting things going on in the scientific

community. This caption will appear next to sites that contain

interesting topics in the news to highlight what biology students can

do in the lab at Penn State or in a job post-graduation!

o The library at Penn State has proved to be invaluable for accessing

sites that students would usually have to purchase site access. This

caption will indicate sites that should be accessed through

libraries.psu.edu, located under the databases tab, unless one would

like to pay for their own access!

Resources Found in this Guide

In the sections below, one will find resources pertinent to the biological studies.

Within each main category, sites for upperclassmen use are listed first, with

subsequent sites suited for students of different semester standings. Remember to

pay attention to graphics for recommended site usage.

About this Guide

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General Internet Sites

RCSB Protein Data Bank

http://www.rcsb.org/pdb/home/home.do

Abstract: Students researching macromolecular structure of proteins will benefit

greatly from this site. The Protein Data Bank (PBD) is a comprehensive archive of

biological macromolecules such as DNAs, RNAs, and proteins. This resource is

also essential to biochemists as it allows for viewing secondary, tertiary, and

quaternary structures of proteins and keys motifs within a specific protein.

Searching within this site is made easy by the "Explore Archive" option that allows

browsing by polymer type, taxonomy, and enzyme classification, to mention a few.

Tips for using this site:

To download structures click on the "Download Files" link under the section

titled "Tools." Enter the PDB IDs and separate them by commas to retrieve

the desired structures.

To obtain multiple file formats of the molecule, such as NMR restraints,

mark the check boxes in the preceding pointer and click "Next." Save the

files to a flash drive or to the desktop.

One can also compare structures of molecules under the "Tools" section.

Once one follows that link, fill in the two provided boxes with the two

polypeptides in question, select the comparison method, and click compare.

Job listings by PBD can also be found by clicking on "Careers" under the

"Home" box on the left. This is a great resource for a student looking for a

career; PBD is currently looking for potential employees with a B.S. in

biology or biochemistry!

General Internet Sites

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PROSITE Protein Database

http://prosite.expasy.org/

Abstract: This site provides a very useful tool for students running protein assays.

It consists of a search box for the input of protein names and allows for quick

viewing of consensus sequences and contains documentation entries for domains,

homologs, and functional sites. Additionally, one can scan sequences against

PROSITE patterns and profiles with the option of an advanced scan. This site is

great for viewing peptide sequences for quick identification of important residue

R-groups.

Tips for using this site:

In the search box, on the left hand side, type the name of a protein of interest

to retrieve a description of its action in the cell, including its peptide

sequence.

One can also browse the data bank of proteins by clicking on one of the four

links under the "Browse" section located in the middle of the page.

To compare one's sequence, enter the peptide sequence in the box located at

the bottom left corner and click "Scan."

General Internet Sites

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BioOne

http://www.bioone.org

Abstract: This website contains a wealth of bioscience research journals for many

fields of biology including, but not limited to, teaching, embryology, zoology, and

cell biology. Journals are listed alphabetically by title, publisher, or collection that

allows for a broad search. When visiting this site, expect an easy-to-use search tool

that helps narrow results for quick journal evaluations. Journal articles are

downloadable as PDF files or can be viewed directly on the webpage. Overall, this

site has excellent content organization, provides user-friendly browsing tools, and

offers a multitude of research journals for any biological discipline.

Tips for using this site:

This sites simplicity compliments its effective search tool. To search for a

journal article click on "Advanced Search" in the upper right hand corner of

the screen. An expanded search box will then appear on the left.

One can also save a search and view it later by inputting a name and

description in the box beneath the search tool.

There are several browsing modes as well. One can browse by title,

publisher, or collection by selecting and option from the "Browse" link.

General Internet Sites

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Biology News Net

www.biologynews.net

Abstract: Any biologist looking to follow current and interesting news in biology

can rely on this site to deliver it. This site concisely presents news in biological

research and further captures the reader's interest with visually stimulating

graphics. In addition, the news articles offer easy readability for any person that

might not specialize in biology but is interested in the topic. The site also provides

links to many other scientific sites and discussion rooms for further topical

investigation. Overall, this site keeps a biologist up-to-date with current research in

biology, such as epigenetic regulation of oncogenes, which is great for research

brainstorming.

Tips for using this site:

To view articles click on the "Full article" link located at the bottom of the

article summary. To get back to the home page where other articles are

listed, click on the large Biology News Net banner on the left.

A fun item to mention on this site is the view counter located on the lower

left of each article box to show how many other people have accessed that

article. It offers a good way to gauge how interesting that article might be!

General Internet Sites

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Publications

Journal of Cell Biology

http://jcb.rupress.org/

Abstract: The Journal of Cell Biology is a great resource, especially for

upperclassmen, on research in intracellular signaling, such as directed chromatin

signaling, proteomics, and genomics. This site puts the latest articles at one's

fingertips and offers a section titled "Research Highlights" in which it gives a brief

synopsis of the study and a link for further reading. In addition, there are many

links to news, multimedia, and an archive of previous publications. This site has

been previously recommended by a professor of biology, a good indicator to its

importance and significance.

Tips for using this site:

On the left hand side of the site the current issue is displayed. Click on the

"View Table of Contents" link. All the articles in that month's issue will be

present with abstracts. To see the abstracts, all one needs to do is hover the

cursor over the article title.

The site also contains alerts and feeds to help one stay current with research

published in this journal. Click on "alerts & feeds" to subscribe to a feed

such as Facebook or Twitter.

One can also access the Journal of Experimental Medicine or the Journal of

General Physiology, hyperlinked in tabs on the upper right of the site. There

will be some overlap of content, but they are two other great sources for

primary literature and leading research.

Publications

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Thomson Reuters Web of KnowledgeSM

apps.webofknowledge.com

Web Of Knowledge SM

is an online index for fast searching of journals and

databases. It includes three search parameters that help fine-tune document

searching.

Abstract: Web Of Knowledge SM

contains a great database called Biological

Abstracts® that serves as a search engine for published research. This site should

be of particular interest to cell biologists and biochemists since these categories

contain the greatest amount of publications. For instance, if one searches for BRaf,

the site lists publications that discuss the oncogene and its prevalence in

melanocytic nevi. Nonetheless, this site empowers one with efficient browsing and

for less time on the web and more time in the lab.

Tips for using this site:

Most importantly, access this site via libraries.psu.edu and click on

databases. Select "B" to list databases starting with that letter and

click on "Biological Abstracts." This will give one full access to the

site.

A unique feature of this site is its guided search. It allows the user to

choose a broad category of interest and refine search results with

subcategories. First, enter the search word or phrase and wait for the

results to load. Second, on the left hand side of the page is a blue box

for search refinement, select boxes in the "Subject Areas" section and

click "Refine."

If one wishes to save their search, click on the link "Search History"

and select the searches you wish to save. Save the searches to a flash

drive for later access.

Publications

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The Statistical Abstract of the United States

http://www.census.gov/compendia/statab/

Abstract: This site offers a summary of statistics on the social, political, and

economic organization of the United States. The site provides a wealth of data for

students interested in a statistical representation of occupational employment in

one's field. The site categorizes this data under sections on the left hand side of the

page. The information included also serves as a guide to other statistical

publications available to the public. Follow the example below to find life sciences

(biology falls in this category) and healthcare related job growth.

Example:

http://www.census.gov/compendia/statab/2011/tables/11s0813.pdf

Click on the above link to find statistics on employment, earnings, and growth in

science. This will load a PDF document representing a table from the Bureau of

Labor Statistics' Occupational Employment Survey. Of particular interest is the job

growth for the life scientist. According to the table, there was a mean annual

growth of 3.7% for Life Scientists. One can use this table to compare job growths

and use it to evaluate future job opportunities.

Tips for using this site:

On the left hand side of the page scroll down and click on "Science and

Technology." Another box will pop up, click on "Employment." This will

take one to statistical data for employment in the sciences.

On the right hand side of the page are useful links for further investigations.

Population ecologists might find it useful to click on the "Births and Deaths"

link as it provides interesting statistics about the U.S. growth rate. One could

use it to postulate when the U.S. reach its carrying capacity.

Publications

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Catalog of U.S. Government Publications

http://catalog.gpo.gov/

Abstract: The Catalog of U.S. Government Publications (GCP) is a search tool for

finding publications from the U.S. government agencies. Users can enter words or

phrases under the advanced search option, which often yields more than enough

results. For instance, users can type in different viral strains of the flu or smallpox

and find hundreds of articles on its use in bioterrorism or its epidemiology .

Moreover students studying ecology could use it to look up literature on a specific

species of bird. Overall, the site is easy to navigate with tabs located at the top to

search different pages quickly. Ecology students, see the below example for a

document on Mountain Plovers, a threatened species of bird.

Example:

Title: Mountain Plover (Charadrius montanus)

Publisher: Wildlife Habitat Management Institute

Author: Holly L. May

Reviewed by: Fritz Knopf

This document outlines habitat requirements of the mountain plover and how

landowners can develop a species-specific management plan. Moreover, the

document lists behaviors, such as polyandry, ranges, and habitat requirements for

mountain plovers, which is critical in the preservation of this threatened species.

This article is a great example of a document that can be cited in one's own

introduction in a research paper. Furthermore, the document was reviewed by Fritz

Knopf, a well-known ornithologist and has done much of his own research on this

species.

Tip for using this site:

This site is really basic, just click on the "Advanced" tab to bring up a quick

search for a topic of interest!

Multiple search parameters will show up under this tab, one should keep the

search simple and sort the results by date to show the most recent updates.

One can also select multiple documents for viewing by selecting the

respective check boxes and clicking "View Selected."

Publications